DMR.plot() Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
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0
Entering edit mode
Chiara • 0
@42efd8d7
Last seen 8 months ago
Norway

Hi!

I'm performing methylation analysis using DMRcate to find the differentially methylated regions. I would now like to plot the fist DMR using DMR.plot(). However when I run it I get the following error: Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie. Any suggestions on how to solve this error?


DMR.plot(ranges=results.ranges1, dmr=1, CpGs=getBeta(GRSet.norm.na.good.noSnp.noXreact), what="Beta", arraytype = "EPIC", phen.col=cols, genome="hg19")
Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie


sessionInfo( )
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.0

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Oslo
tzcode source: internal

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DMRcatedata_2.18.0                                  ExperimentHub_2.8.1                                
 [3] AnnotationHub_3.8.0                                 BiocFileCache_2.8.0                                
 [5] dbplyr_2.3.4                                        IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
 [7] minfi_1.46.0                                        bumphunter_1.42.0                                  
 [9] locfit_1.5-9.8                                      iterators_1.0.14                                   
[11] foreach_1.5.2                                       Biostrings_2.68.1                                  
[13] XVector_0.40.0                                      SummarizedExperiment_1.30.2                        
[15] Biobase_2.60.0                                      MatrixGenerics_1.12.3                              
[17] matrixStats_1.0.0                                   GenomicRanges_1.52.1                               
[19] GenomeInfoDb_1.36.4                                 IRanges_2.34.1                                     
[21] S4Vectors_0.38.2                                    BiocGenerics_0.46.0                                
[23] DMRcate_2.14.1                                      BiocManager_1.30.22                                
[25] ggplot2_3.4.4                                       corrplot_0.92                                      
[27] rstatix_0.7.2                                       dplyr_1.1.3                                        

loaded via a namespace (and not attached):
  [1] splines_4.3.1                                      later_1.3.1                                       
  [3] BiocIO_1.10.0                                      bitops_1.0-7                                      
  [5] filelock_1.0.2                                     cellranger_1.1.0                                  
  [7] tibble_3.2.1                                       R.oo_1.25.0                                       
  [9] preprocessCore_1.62.1                              XML_3.99-0.14                                     
 [11] rpart_4.1.21                                       lifecycle_1.0.3                                   
 [13] edgeR_3.42.4                                       base64_2.0.1                                      
 [15] MASS_7.3-60                                        lattice_0.21-9                                    
 [17] ensembldb_2.24.1                                   scrime_1.3.5                                      
 [19] backports_1.4.1                                    magrittr_2.0.3                                    
 [21] limma_3.56.2                                       Hmisc_5.1-1                                       
 [23] rmarkdown_2.25                                     yaml_2.3.7                                        
 [25] httpuv_1.6.12                                      doRNG_1.8.6                                       
 [27] askpass_1.2.0                                      Gviz_1.44.2                                       
 [29] DBI_1.1.3                                          RColorBrewer_1.1-3                                
 [31] abind_1.4-5                                        zlibbioc_1.46.0                                   
 [33] quadprog_1.5-8                                     purrr_1.0.2                                       
 [35] R.utils_2.12.2                                     AnnotationFilter_1.24.0                           
 [37] biovizBase_1.48.0                                  RCurl_1.98-1.12                                   
 [39] nnet_7.3-19                                        VariantAnnotation_1.46.0                          
 [41] rappdirs_0.3.3                                     GenomeInfoDbData_1.2.10                           
 [43] genefilter_1.82.1                                  annotate_1.78.0                                   
 [45] permute_0.9-7                                      DelayedMatrixStats_1.22.6                         
 [47] codetools_0.2-19                                   DelayedArray_0.26.7                               
 [49] xml2_1.3.5                                         tidyselect_1.2.0                                  
 [51] beanplot_1.3.1                                     base64enc_0.1-3                                   
 [53] illuminaio_0.42.0                                  GenomicAlignments_1.36.0                          
 [55] multtest_2.56.0                                    ellipsis_0.3.2                                    
 [57] Formula_1.2-5                                      survival_3.5-7                                    
 [59] missMethyl_1.34.0                                  tools_4.3.1                                       
 [61] progress_1.2.2                                     Rcpp_1.0.11                                       
 [63] glue_1.6.2                                         gridExtra_2.3                                     
 [65] xfun_0.40                                          HDF5Array_1.28.1                                  
 [67] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1 withr_2.5.1                                       
 [69] fastmap_1.1.1                                      latticeExtra_0.6-30                               
 [71] rhdf5filters_1.12.1                                fansi_1.0.5                                       
 [73] openssl_2.1.1                                      digest_0.6.33                                     
 [75] R6_2.5.1                                           mime_0.12                                         
 [77] colorspace_2.1-0                                   gtools_3.9.4                                      
 [79] jpeg_0.1-10                                        dichromat_2.0-0.1                                 
 [81] biomaRt_2.56.1                                     RSQLite_2.3.1                                     
 [83] R.methodsS3_1.8.2                                  utf8_1.2.4                                        
 [85] tidyr_1.3.0                                        generics_0.1.3                                    
 [87] data.table_1.14.8                                  rtracklayer_1.60.1                                
 [89] prettyunits_1.2.0                                  httr_1.4.7                                        
 [91] htmlwidgets_1.6.2                                  S4Arrays_1.0.6                                    
 [93] pkgconfig_2.0.3                                    gtable_0.3.4                                      
 [95] blob_1.2.4                                         siggenes_1.74.0                                   
 [97] htmltools_0.5.6.1                                  carData_3.0-5                                     
 [99] ProtGenerics_1.32.0                                scales_1.2.1                                      
[101] png_0.1-8                                          knitr_1.44                                        
[103] rstudioapi_0.15.0                                  tzdb_0.4.0                                        
[105] rjson_0.2.21                                       nlme_3.1-163                                      
[107] checkmate_2.2.0                                    curl_5.1.0                                        
[109] org.Hs.eg.db_3.17.0                                cachem_1.0.8                                      
[111] rhdf5_2.44.0                                       stringr_1.5.0                                     
[113] BiocVersion_3.17.1                                 foreign_0.8-85                                    
[115] AnnotationDbi_1.62.2                               restfulr_0.0.15                                   
[117] GEOquery_2.68.0                                    reshape_0.8.9                                     
[119] pillar_1.9.0                                       grid_4.3.1                                        
[121] vctrs_0.6.4                                        promises_1.2.1                                    
[123] car_3.1-2                                          xtable_1.8-4                                      
[125] cluster_2.1.4                                      htmlTable_2.4.1                                   
[127] evaluate_0.22                                      bsseq_1.36.0                                      
[129] readr_2.1.4                                        GenomicFeatures_1.52.2                            
[131] cli_3.6.1                                          compiler_4.3.1                                    
[133] Rsamtools_2.16.0                                   rngtools_1.5.2                                    
[135] rlang_1.1.1                                        crayon_1.5.2                                      
[137] nor1mix_1.3-0                                      mclust_6.0.0                                      
[139] interp_1.1-4                                       plyr_1.8.9                                        
[141] stringi_1.7.12                                     deldir_1.0-9                                      
[143] BiocParallel_1.34.2                                munsell_0.5.0                                     
[145] lazyeval_0.2.2                                     DSS_2.48.0                                        
[147] Matrix_1.6-1.1                                     BSgenome_1.68.0                                   
[149] hms_1.1.3                                          sparseMatrixStats_1.12.2                          
[151] bit64_4.0.5                                        Rhdf5lib_1.22.1                                   
[153] statmod_1.5.0                                      KEGGREST_1.40.1                                   
[155] shiny_1.7.5.1                                      interactiveDisplayBase_1.38.0                     
[157] broom_1.0.5                                        memoise_2.0.1                                     
[159] bit_4.0.5                                          readxl_1.4.3
DMRcate DMR.plot • 841 views
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0
Entering edit mode
shepherl 3.9k
@lshep
Last seen 12 hours ago
United States

Please see response on bioc-devel mailing list
https://stat.ethz.ch/pipermail/bioc-devel/2023-October/019973.html

It was a known issue with rtracklayer; The PR was merged so it should hopefully resolve soon.

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